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Structure of reduced cytochrome C6 from synechococcus sp. pcc 7002

Analyse Structure of reduced cytochrome C6 from synechococcus sp. pcc 7002 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DR0
Type: protein
Length: 279 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C6
UniProt: O30881
Ligands: HEM, SO4
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Cytochrome C6	protein	93	56% helix, 4% strand	O30881

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 2 copies · chains B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	191	0.71	0.88	31	HEM
2	304	0.71	0.84	44	HEM
3	200	0.70	0.87	30	HEM

Interfaces

2 interfaces between chains.

B–C · 381 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 139 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 cofactor (heme attachment).

Compared structures

3DR0 · Structure of reduced cytochrome c6 from Synechococcus sp. PCC 7002 · the same entry in another collection · chain B against B, TM-score 1.00
O30881 · AlphaFold monomer V2.0 prediction for cytochrome C6 (O30881) · a predicted model of the same protein · chain A against A, TM-score 0.99

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O30881
Elsewhere: RCSB PDB 3DR0 · PDBe 3DR0 · UniProt O30881

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